Use of Next Generation Sequencing to Investigate the Genomics of Bacterial Pathogens.

This thesis explores the use of next generation sequencing as a tool to investigate the genomics of bacterial pathogens of plants and humans. Firstly, second-generation sequencing was applied to the evolution of distantly related bacterial species that have converged on common host plants (Xanthomonas bacteria on sugarcane and common-bean plants). This revealed evidence of recent horizontal gene transfer between X. phaseoli pv. phaseoli and X. citri pv. fuscans and between X. axonopodis pv. vasculorum and X. vasicola. distantly related sugarcane pathogens. Furthermore, we discovered that strains isolated from lablab bean (a close relative of common bean) form a previously unknown third distinct clade (and perhaps pathovar) and whole-genome comparisons suggested horizontal gene transfer played an important role in the evolution of host specificity in xanthomonad pathogens. Next, second-generation sequencing was used to rapidly gain insight into novel emerging bacterial pathogens, namely unusually virulent Asian strains of the human pathogen Campylobacter jejuni and a xanthomonad causing unusual symptoms on common bean in African country of Rwanda. A type six secretion system was shown to be associated with a more serious form of campylobacteriosis and a molecular marker for an intact type six secretion system was identified. This was shown to be more prevalent in strains isolated from Asia than strains isolated in the UK, a finding which has serious implications for chicken import. Further to this the genome sequence of a newly emerging Xanthomonas bean pathogen isolated from a recent outbreak in Rwanda is presented. Analysis of the Rwandan Xanthomonas genome shows it represents the first sequenced isolate in a novel species level clade, which was subsequently named as Xanthomonas cannabis and is genetically distinct from previously known bean pathogens. Lastly, the performance of the third-generation sequencing platform Oxford Nanopore MinION was assessed which will prove to be an exciting resource to perform bacterial genomic studies in the future. In summary, this work exemplifies the value of sequencing-based approaches for rapidly and cheaply gaining insights into evolution of bacterial pathogen